Update online docs to 1.0.5

9 files changed, 32 insertions, 35 deletions

diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html
index 3b6ae721..542599da 100644
--- a/docs/reference/dimethenamid_2018.html
+++ b/docs/reference/dimethenamid_2018.html
@@ -77,7 +77,7 @@ constrained by data protection regulations." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
@@ -162,13 +162,13 @@ constrained by data protection regulations.</p>
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <a href='mkindsg.html'>mkindsg</a> object grouping eight datasets with some meta information</p>
+    <p>An <a href='mkindsg.html'>mkindsg</a> object grouping seven datasets with some meta information</p>
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018)
 Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour
 Rev. 2 - November 2017
-<a href='http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211'>http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211</a></p>
+<a href='https://open.efsa.europa.eu'>https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a></p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>The R code used to create this data object is installed with this package
@@ -177,33 +177,30 @@ specific pieces of information in the comments.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>dimethenamid_2018</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 8 mkinds objects
+</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 7 mkinds objects
 #&gt; Title $title:  Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 
 #&gt; Occurrence of observed compounds $observed_n:
 #&gt; DMTAP   M23   M27   M31  DMTA 
-#&gt;     4     7     7     7     4 
+#&gt;     3     7     7     7     4 
 #&gt; Time normalisation factors $f_time_norm:
-#&gt; [1] 1.0000000 0.9706477 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922
-#&gt; [8] 0.6733938
+#&gt; [1] 1.0000000 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922 0.6733938
 #&gt; Meta information $meta:
-#&gt;                       study  usda_soil_type study_moisture_ref_type
-#&gt; Calke         Unsworth 2014      Sandy loam                     pF2
-#&gt; Borstel 1 Staudenmaier 2013            Sand                     pF1
-#&gt; Borstel 2 Staudenmaier 2009            Sand                     pF1
-#&gt; Elliot 1         Wendt 1997       Clay loam                   pF2.5
-#&gt; Elliot 2         Wendt 1997       Clay loam                   pF2.5
-#&gt; Flaach           König 1996 Sandy clay loam                     pF1
-#&gt; BBA 2.2          König 1995      Loamy sand                     pF1
-#&gt; BBA 2.3          König 1995      Sandy loam                     pF1
-#&gt;           rel_moisture study_ref_moisture temperature
-#&gt; Calke             1.00                 NA          20
-#&gt; Borstel 1         0.50              23.00          20
-#&gt; Borstel 2         0.50              23.00          20
-#&gt; Elliot 1          0.75              33.37          23
-#&gt; Elliot 2          0.75              33.37          23
-#&gt; Flaach            0.40                 NA          20
-#&gt; BBA 2.2           0.40                 NA          20
-#&gt; BBA 2.3           0.40                 NA          20</div></pre>
+#&gt;                      study  usda_soil_type study_moisture_ref_type rel_moisture
+#&gt; Calke        Unsworth 2014      Sandy loam                     pF2         1.00
+#&gt; Borstel  Staudenmaier 2009            Sand                     pF1         0.50
+#&gt; Elliot 1        Wendt 1997       Clay loam                   pF2.5         0.75
+#&gt; Elliot 2        Wendt 1997       Clay loam                   pF2.5         0.75
+#&gt; Flaach          König 1996 Sandy clay loam                     pF1         0.40
+#&gt; BBA 2.2         König 1995      Loamy sand                     pF1         0.40
+#&gt; BBA 2.3         König 1995      Sandy loam                     pF1         0.40
+#&gt;          study_ref_moisture temperature
+#&gt; Calke                    NA          20
+#&gt; Borstel               23.00          20
+#&gt; Elliot 1              33.37          23
+#&gt; Elliot 2              33.37          23
+#&gt; Flaach                   NA          20
+#&gt; BBA 2.2                  NA          20
+#&gt; BBA 2.3                  NA          20</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index a83276f3..bfe030b0 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 36ef6367..ff7a4198 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html
index b4f8db16..b3bf35bf 100644
--- a/docs/reference/mixed.html
+++ b/docs/reference/mixed.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index cda53ce8..f9976c6b 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -78,7 +78,7 @@ mkinmod." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
@@ -348,7 +348,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
    parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
    m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span>,
    name <span class='op'>=</span> <span class='st'>"SFO_SFO"</span>, dll_dir <span class='op'>=</span> <span class='va'>DLL_dir</span>, unload <span class='op'>=</span> <span class='cn'>TRUE</span>, overwrite <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/RtmpQCjjOu/filef8c1f2031f4ea.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
+</div><div class='output co'>#&gt; <span class='message'>Copied DLL from /tmp/Rtmp1acwPp/fileb9e34769fb8fe.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span></div><div class='input'><span class='co'># Now we can save the model and restore it in a new session</span>
 <span class='fu'><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS</a></span><span class='op'>(</span><span class='va'>SFO_SFO.2</span>, file <span class='op'>=</span> <span class='st'>"~/SFO_SFO.rds"</span><span class='op'>)</span>
 <span class='co'># Terminate the R session here if you would like to check, and then do</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://pkgdown.jrwb.de/mkin/'>mkin</a></span><span class='op'>)</span>
@@ -397,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&gt;     })
 #&gt;     return(predicted)
 #&gt; }
-#&gt; &lt;environment: 0x55555a59b978&gt;</div><div class='input'>
+#&gt; &lt;environment: 0x55555a720040&gt;</div><div class='input'>
 <span class='co'># If we have several parallel metabolites</span>
 <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
 <span class='va'>m_synth_DFOP_par</span> <span class='op'>&lt;-</span> <span class='fu'>mkinmod</span><span class='op'>(</span>
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index c6b43aab..6821bacf 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 03448606..b3052605 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html
index b75fa6e6..090a644c 100644
--- a/docs/reference/plot.mixed.mmkin.html
+++ b/docs/reference/plot.mixed.mmkin.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>
 
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index c6d716a1..e195d8bf 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -79,7 +79,7 @@ below to see their documentation.
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.5</span>
       </span>
     </div>